[gmx-users] number of grid cells is zero

najwa drici dricinajwa at hotmail.fr
Sun Jul 27 19:54:34 CEST 2008

i want to ask you question about how can i deprotonate or use deprotonated cysteine because I have protein with “cys” in active site, and I want to use deprotonated“cys”. when i run “pdb2gmx “  no option appearing of choosing Cys deprotonated state possibility > Date: Sun, 27 Jul 2008 13:16:20 +0200> From: spoel at xray.bmc.uu.se> To: gmx-users at gromacs.org> Subject: Re: [gmx-users] number of grid cells is zero> > N. Sundar Ram wrote:> > Hi everyone,> > I am a new user of gromacs. I am running MD for a Pleckstrin> > homology domain (100 amino acids) in 8 nodes (32 CPUs). After> > Mdurn i get the following error: "Number of grid cells is> > zero. system is collapsing".> > Though I saw many mails regarding this problem in the mailing list, I> > could not get a proper answer.> > > > Can anyone please tell me what should I do to get it running.> > > > Thanking you in advance.> fix the problems in your structure most likely. Did you say homology?> check the wiki.> > -- > David van der Spoel, Ph.D., Professor of Biology> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se> _______________________________________________> gmx-users mailing list gmx-users at gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please search the archive at http://www.gromacs.org/search before posting!> Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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